Commit 42bdcd08 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

update README

parent c99581e0
......@@ -2,10 +2,14 @@
## From raw fastq data to vcf file.
## Pipeline features:
### 1) read preprocessing,
### 2) reads QC,
### 3) mapping with bwa,
### 4) mapping QC
### 5) SNPs calling using GATK in parallel mode: reference splitted by sequences: #tasks=#samples X #chrs
### 2) reads QC, fastq report
### 3) merges overlaping read and keep unmerged Paired end (R1 & R2)
### 4) mapping with bwa,
a) maps unmerged reads (PE)
b) maps merged reads
c) merge the 2 bam file
### 5) mapping QC report (multiqc)
### 6) SNPs calling using GATK in parallel mode: reference splitted by sequences: #tasks=#samples X #chrs
## Snakemake features: fastq from csv file, config, modules, SLURM
### Workflow steps are descibed in the dag_rules.pdf
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